[Biopython-dev] Parsing malformed genbank files (e.g. VectorNTI)

[Timothy Ham]

Hi everyone,

The current biopython GenBank parser dies while parsing VectorNTI
generated files.  For example, until recently, BioPython did not
accept an empty SOURCE field. It still does not handle an empty
VERSION or ACCESSION fields (consumer.data.id never gets filled),
which is the default for user generated vector maps via VectorNTI.

Now, it is easy enough to change the GenBank parser to handle
malformed genbank files, (I can submit patches) but the real question
becomes:
> Should BioPython handle malformed genbank files at all?
I would like to be practical and say yes, since VectorNTI is a very
common, widely used format, but I wanted to ask the community before
submitting my patches.

Thanks for the great work,
Tim